Locus 1942

Sequence ID	2L_DroMel_CAF1
Location	5,253,675 – 5,253,796
Length	121
Max. P	0.870163

overview

Window 9

Location	5,253,675 – 5,253,777
Length	102
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.46
Mean single sequence MFE	-34.27
Consensus MFE	-16.70
Energy contribution	-17.32
Covariance contribution	0.61
Combinations/Pair	1.06
Mean z-score	-1.74
Structure conservation index	0.49
SVM decision value	-0.02
SVM RNA-class probability	0.525293
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5253675 102 + 22407834
----CUCCAGCUACUCGUCGUUUGAACCC----------GU----CCCGAGUGCAGCCCCAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCCUGGCCGGCAGACGUGGCUGGAAUUUUA
----.(((((((((((((((.........----------..----...(((.((.........))))).........((((.(((.....))))))))))).)).)))))))))...... ( -32.80)
>DroPse_CAF1 28810 112 + 1
GCUACUCCUUCUACUC---CUUGGCGGACCUUCGGUUG-GG----GCCUGGGGUAGCCCUAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCUUGGCCGCCAAACGUGGCUGGAAUUUUA
.....(((..((((..---.(((((((.((..((((((-((----((........))))))).(((((............)))))...)))...)))))))))..))))..)))...... ( -39.30)
>DroEre_CAF1 23393 99 + 1
----CUGCAGCUACUC---GUCUGAACCC----------GU----CUUGAGAGCAGCCCUAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCCUGGCCGGCAGACGUGGCUGGAAUUUUA
----...(((((((..---(((((...((----------(.----.(((((.((.........)).)))))......((((.(((.....))))))))))))))))))))))........ ( -31.10)
>DroYak_CAF1 32469 107 + 1
---GCUCCAGCUACUC---GUUUGAAGCUCUUGAA-A--GU----CUUGAGAGCAGCCCUAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCCUGGCCGACAGACGUGGCUGGAAUUUUA
---..(((((((((..---(((((..(((((..(.-.--..----.)..))))).......................((((.(((.....)))))))...))))))))))))))...... ( -39.60)
>DroAna_CAF1 11710 112 + 1
---GCUCCUGCUCCUU---GCUUGCUCCU-UUGAA-UGCUACUUUUUUUCUUCCUGCCCCAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCCGGGCCGGCCGACGUGGCUGGAAUUUUA
---..(((.((...((---((((((....-(((((-.(((......................))).)))))......))..))))))...)).)))((((((.....))))))....... ( -23.55)
>DroPer_CAF1 28891 112 + 1
GCUACUCCUUCUACUC---CUUGGCGGACCUUCGGUUG-GG----GCCUGGGGUAGCCCUAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCUUGGCCGCCAAACGUGGCUGGAAUUUUA
.....(((..((((..---.(((((((.((..((((((-((----((........))))))).(((((............)))))...)))...)))))))))..))))..)))...... ( -39.30)
>consensus
____CUCCAGCUACUC___GUUUGAACCC_UU____U__GU____CCCGAGAGCAGCCCUAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCCUGGCCGGCAGACGUGGCUGGAAUUUUA
.....(((.(((((.........................................((......))............((((.(((.....)))))))........))))).)))...... (-16.70 = -17.32 +   0.61)

alignment

secondary structure

dotplot

Window 0

Location	5,253,675 – 5,253,777
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.46
Mean single sequence MFE	-33.48
Consensus MFE	-20.50
Energy contribution	-20.28
Covariance contribution	-0.22
Combinations/Pair	1.12
Mean z-score	-1.29
Structure conservation index	0.61
SVM decision value	0.03
SVM RNA-class probability	0.546357
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5253675 102 - 22407834
UAAAAUUCCAGCCACGUCUGCCGGCCAGGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUGGGGCUGCACUCGGG----AC----------GGGUUCAAACGACGAGUAGCUGGAG----
......((((((..((((.(((.(((((((.....))).))))...........)))((((((.((((......)----.)----------)).)))))).))))....)))))).---- ( -34.50)
>DroPse_CAF1 28810 112 - 1
UAAAAUUCCAGCCACGUUUGGCGGCCAAGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUAGGGCUACCCCAGGC----CC-CAACCGAAGGUCCGCCAAG---GAGUAGAAGGAGUAGC
....(((((..(.((.((((((((((...((....(((((............)))))....(((((......)))----))-....))..)).))))))))---..)).)..)))))... ( -38.00)
>DroEre_CAF1 23393 99 - 1
UAAAAUUCCAGCCACGUCUGCCGGCCAGGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUAGGGCUGCUCUCAAG----AC----------GGGUUCAGAC---GAGUAGCUGCAG----
........((((..((((((((((((((((.....))).))))...........((((....)))).........----.)----------))...)))))---)....))))...---- ( -30.30)
>DroYak_CAF1 32469 107 - 1
UAAAAUUCCAGCCACGUCUGUCGGCCAGGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUAGGGCUGCUCUCAAG----AC--U-UUCAAGAGCUUCAAAC---GAGUAGCUGGAGC---
.....((((((((.((.....))(((((((.....))).))))...........))))....((((((((..(((----.(--(-(....)))))).....---)))))))))))).--- ( -33.60)
>DroAna_CAF1 11710 112 - 1
UAAAAUUCCAGCCACGUCGGCCGGCCCGGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUGGGGCAGGAAGAAAAAAAGUAGCA-UUCAA-AGGAGCAAGC---AAGGAGCAGGAGC---
.....((((.(((.((((((.....))))))....(((((............))))).....))).))))...........((.-((...-..))))..((---.....))......--- ( -26.50)
>DroPer_CAF1 28891 112 - 1
UAAAAUUCCAGCCACGUUUGGCGGCCAAGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUAGGGCUACCCCAGGC----CC-CAACCGAAGGUCCGCCAAG---GAGUAGAAGGAGUAGC
....(((((..(.((.((((((((((...((....(((((............)))))....(((((......)))----))-....))..)).))))))))---..)).)..)))))... ( -38.00)
>consensus
UAAAAUUCCAGCCACGUCUGCCGGCCAGGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUAGGGCUGCACUAAAG____AC__A____AA_GGCUGCAAAC___GAGUAGCAGGAG____
........(((((.((((((.....))))))....(((((............))))).....)))))..................................................... (-20.50 = -20.28 +  -0.22)

alignment

secondary structure

dotplot

Window 1

Location	5,253,701 – 5,253,796
Length	95
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.83
Mean single sequence MFE	-28.74
Consensus MFE	-18.01
Energy contribution	-18.15
Covariance contribution	0.14
Combinations/Pair	1.14
Mean z-score	-1.65
Structure conservation index	0.63
SVM decision value	0.61
SVM RNA-class probability	0.799768
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5253701 95 + 22407834
U----CCCGAGUGCAGCCCCAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCCUGGCCGGCAGACGUGGCUGGAAUUUUAAAUGUAUUUUU----CAGCCACA-----------------
.----.(((((.((.........))))..........((((.(((.....)))))))))).....((((((((((.............)))----))))))).----------------- ( -29.02)
>DroPse_CAF1 28846 116 + 1
G----GCCUGGGGUAGCCCUAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCUUGGCCGCCAAACGUGGCUGGAAUUUUAAAUGUAUUUCAACAACAGCCACAGCCACAGCCAUAGCCAC
(----((.(((((..(((...((((.((......))(((....)))....)))))))..))....(((((((.......................)))))))..)))..)))........ ( -32.60)
>DroEre_CAF1 23416 95 + 1
U----CUUGAGAGCAGCCCUAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCCUGGCCGGCAGACGUGGCUGGAAUUUUAAAUGUAUUUUU----CAGCCACA-----------------
.----..........(((.((((........))))..((((.(((.....))))))).)))....((((((((((.............)))----))))))).----------------- ( -29.82)
>DroYak_CAF1 32500 95 + 1
U----CUUGAGAGCAGCCCUAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCCUGGCCGACAGACGUGGCUGGAAUUUUAAAUGUAUUUUU----CAGCCACA-----------------
.----.(((((.((.........)).)))))......((((.(((.....)))))))........((((((((((.............)))----))))))).----------------- ( -27.12)
>DroAna_CAF1 11742 100 + 1
ACUUUUUUUCUUCCUGCCCCAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCCGGGCCGGCCGACGUGGCUGGAAUUUUAAAUGUAUUUCUG---CGUCCAGA-----------------
.............(((.(((...((.((......)).))...(((.....))))))((((((.....))))))........(((((....))---))).))).----------------- ( -21.30)
>DroPer_CAF1 28927 116 + 1
G----GCCUGGGGUAGCCCUAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCUUGGCCGCCAAACGUGGCUGGAAUUUUAAAUGUAUUUCAACAACAGCCACAGCCACAGCCAUAGCCAC
(----((.(((((..(((...((((.((......))(((....)))....)))))))..))....(((((((.......................)))))))..)))..)))........ ( -32.60)
>consensus
U____CCCGAGAGCAGCCCUAAAGCCUUUAAUUUAAUGCCAAGGCAAUUCGCCUGGCCGGCAGACGUGGCUGGAAUUUUAAAUGUAUUUCU____CAGCCACA_________________
.....................................((((.(((.....)))))))........(((((((.......................))))))).................. (-18.01 = -18.15 +   0.14)

alignment

secondary structure

dotplot

Window 2

Location	5,253,701 – 5,253,796
Length	95
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.83
Mean single sequence MFE	-31.66
Consensus MFE	-21.36
Energy contribution	-20.08
Covariance contribution	-1.27
Combinations/Pair	1.27
Mean z-score	-1.64
Structure conservation index	0.67
SVM decision value	0.87
SVM RNA-class probability	0.870163
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5253701 95 - 22407834
-----------------UGUGGCUG----AAAAAUACAUUUAAAAUUCCAGCCACGUCUGCCGGCCAGGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUGGGGCUGCACUCGGG----A
-----------------.(((((((----...................))))))).....((((((((((.....))).))))...........((((....)))).....))).----. ( -29.31)
>DroPse_CAF1 28846 116 - 1
GUGGCUAUGGCUGUGGCUGUGGCUGUUGUUGAAAUACAUUUAAAAUUCCAGCCACGUUUGGCGGCCAAGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUAGGGCUACCCCAGGC----C
...(((.(((((((.(.((((((((..(((..((.....))..)))..))))))))..).))))))))))....(((....)))..........(((((..(((....)))))))----) ( -40.50)
>DroEre_CAF1 23416 95 - 1
-----------------UGUGGCUG----AAAAAUACAUUUAAAAUUCCAGCCACGUCUGCCGGCCAGGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUAGGGCUGCUCUCAAG----A
-----------------.(((((((----...................)))))))(((((((.(((((((.....))).))))...........)))....))))..........----. ( -27.21)
>DroYak_CAF1 32500 95 - 1
-----------------UGUGGCUG----AAAAAUACAUUUAAAAUUCCAGCCACGUCUGUCGGCCAGGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUAGGGCUGCUCUCAAG----A
-----------------.(((((((----...................))))))).(((....(((((((.....))).))))...........((((....)))).......))----) ( -25.41)
>DroAna_CAF1 11742 100 - 1
-----------------UCUGGACG---CAGAAAUACAUUUAAAAUUCCAGCCACGUCGGCCGGCCCGGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUGGGGCAGGAAGAAAAAAAGU
-----------------((((....---)))).............((((.(((.((((((.....))))))....(((((............))))).....))).)))).......... ( -27.00)
>DroPer_CAF1 28927 116 - 1
GUGGCUAUGGCUGUGGCUGUGGCUGUUGUUGAAAUACAUUUAAAAUUCCAGCCACGUUUGGCGGCCAAGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUAGGGCUACCCCAGGC----C
...(((.(((((((.(.((((((((..(((..((.....))..)))..))))))))..).))))))))))....(((....)))..........(((((..(((....)))))))----) ( -40.50)
>consensus
_________________UGUGGCUG____AAAAAUACAUUUAAAAUUCCAGCCACGUCUGCCGGCCAGGCGAAUUGCCUUGGCAUUAAAUUAAAGGCUUUAGGGCUGCACUAAAG____A
..................((((((......(((.....)))........((((.((((((.....))))))...(((....)))..........))))....))))))............ (-21.36 = -20.08 +  -1.27)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:32 2006